Samantha Thorne, an android secret agent, has just returned home from a deep-cover assignment to Earth. Her lover, Prime Riordan, is relieved to see her safe after the difficulty they had getting her out without breaking her cover; however, when she downloads her report directly into his brain, she realises that he’s jealous of the year she spent as the lover of the human agent Paul Hunt. Nevertheless, her time with Hunt seems to have confirmed that the Scorpius project is no longer a threat -- or so it seems until the androids receive a distress call from tracking station Beta-4, which is under attack by an Earth Forces raider that has somehow slipped past the front lines. Samantha and Riordan watch helplessly as Cybermen wipe out the crew of Beta-4; it seems that Samantha was wrong, and that Scorpius is an active concern. Even if the androids try to tell the human race what their leaders are doing, their warnings will be dismissed as propaganda; the only way to prove their claims is to have Scorpius exposed by an insider, and that means that Samantha is going to have to go undercover again. As his lover departs after an all-too-brief reunion, Riordan feels despair; if the humans are willing to convert themselves into Cybermen just to defeat the androids, then perhaps there’s no hope for any of them...

Back on Earth, Commander-in-Chief Liam Barnaby is growing upset with the changes to his old friend, President Karen Brett, and he eventually visits the White House to speak with her in person. However, both Brett and the Vice President have unexpectedly gone on tour, leaving Brett’s mysterious advisor, Paul Hunt, in charge. Barnaby protests that Hunt is not an elected official and should not be empowered to make decisions on behalf of the administration, but Hunt brushes aside his concerns. He also refuses to discuss Barnaby’s discovery that secret raiding parties have been sent into android space without Barnaby’s knowledge -- or the fact that the androids have apparently stepped up their propaganda broadcasts, and that all such broadcasts are being jammed and deleted before Barnaby can find out what it is the androids want the humans to believe. Hunt patronisingly informs Barnaby that he’ll have to accept that the President has chosen to keep him out of the loop, and the furious Barnaby storms off before Hunt can make him lose his cool.

Deciding that he needs time to calm down, Barnaby orders his car to drive him home via the scenic ocean route -- but another car speeds up behind him and tries to drive him off the road. Barnaby’s car automatically notifies the emergency services, and his attacker speeds off before they arrive; however, the security chief responding to the call reports that all surveillance cameras along this stretch of highway have gone out, and that Barnaby’s car’s nav-com has somehow had its memory of the incident erased. Shaken by his narrow escape, Barnaby becomes more determined than ever to find out who Paul Hunt really is and what influence he has over Brett. Despite facing a great deal of official obstruction, he manages to access Paul’s personal files and learns that his former residence is now registered to a Samantha Thorne, who currently resides in Oceanic City. Barnaby visits Samantha to ask her about Hunt, whom it turns out was once her lover, but she can give him little useful information. Meanwhile, Hunt discusses the situation with the Cyber-Planner; their overt attempt to kill Barnaby has failed, but Hunt is still capable of more subtle tactics. He thus returns to the White House and informs Brett that Barnaby’s investigation into his past could endanger their attempts to achieve victory in Orion. Brett seems somewhat dazed as she speaks, but she does comprehend that she can’t let anyone, not even Barnaby, get in the way of victory...

Barnaby tries to initiate an official judiciary inquiry into Hunt’s actions, but fails; even the most sympathetic judge, Goran, refuses to question the character of the President’s advisor for fear that it might damage public confidence in the Presidency during a time of war. Brett herself then unexpectedly visits Barnaby in person, but she’s very different from the Brett that he remembers; she’s cold and aloof, and accuses him of abusing his authority to conduct a personal vendetta. To Barnaby’s shock, he realises that his old friend is all but accusing him of preparing to stage a coup against her. Barnaby tries to get through to his old friend, reminding her that they know practically nothing about Hunt or the Scorpius project that he was supposedly involved in; and yet, even as the war in Orion continues to deteriorate, Brett is relying on Hunt more and more and has cut Barnaby out of the loop. He pleads with her one last time to tell her what’s happening, but, as if reciting from a script, she tells him that he’s let his dislike of Paul Hunt cloud his professional judgement. She has already prepared a press release claiming that Barnaby is taking some personal leave, and has brought a security detail with her to escort him out of the White House.

Frustrated, Barnaby contacts Samantha Thorne once again, only to learn that she’s abused her position as a data entry clerk to hack into the White House security net and learn that he’s just been fired. However, she warns him that if he turns her in for the security breach, he’ll never learn the truth about Paul Hunt -- and she also points out that two secret agents have followed him from the White House. She helps him to shake off his pursuers, and he finally accepts that people in his friend’s government may be trying to kill him. Samantha arranges to meet him at the old docks after nightfall to discuss Scorpius; before they part company, she asks him if he’s ever heard of the Cybermen, and doesn’t seem surprised when he hasn’t. Barnaby meets Samantha at the old docks as planned, but he’s been followed by two figures who open fire on them. Samantha manages to get Barnaby to a jet-boat she prepared earlier, and the figures, Cybermen, teleport out before they’re discovered. Samantha informs Barnaby that, when she hacked into the White House security net, she learned that a holographic transmission had been beamed directly to Brett’s living quarters some months ago; she now programmes the boat’s navigator to take her and Barnaby to the transmission’s source. However, both she and Barnaby were struck by blaster fire during their escape -- and as Barnaby passes out from the pain, he realises that Samantha’s wound should have been fatal.

Meanwhile, Earth is being flooded with refugees from the battle zones around Orion, and Hunt is spinning the news reports to make the people of Earth feel helpless and out of control. Soon they’ll be willing to turn anywhere for a solution to the crisis. Brett is beginning to have second thoughts, but Hunt has the ability to erase those doubts and troubling memories from her mind, and soon she’s forgotten all about her friendship with Liam. The Cyber-Planner is (emotionlessly, of course) concerned about Barnaby’s escape, particularly as it seems that he was aided by Hunt’s ex-lover; however, Hunt dismisses Samantha as irrelevant and points out that Barnaby is now a wanted fugitive who will be placed under arrest even if he survived the attack at the docks. Everything is going according to plan; there is nothing to fear.

Barnaby awakens to find that five days have passed; Samantha kept him sedated while his arm healed so he wouldn’t ask awkward questions. To his disgust, she confirms his suspicion that she’s an android spy, and for the first time, she sees up close just how much the humans hate her kind. But there’s nothing Barnaby can do about it, as she’s too fast and strong for him to get past her to the boat’s emergency transmitter -- and nobody in a position of power would listen to him in any case. He has little choice but to listen as she explains that she’s traced the mysterious transmission to the old penal colony on the Isle of Wight -- and despite himself, he is interested when she reveals that the transmission was made by Paul Hunt. Before Samantha can explain further, the penal colony’s newly activated shore defences detect the boat, and Samantha is forced to scuttle it and swim to shore with Barnaby; he still isn’t willing to trust her, but his preconceptions are shaken when a Cyberman walks past them on patrol and he recognises it from the hologram on Reticek IV.

Samantha reveals that the Isle of Wight has been turned into a temporary refugee camp -- but the camp is itself part of the Scorpius project. Unlike humans, androids never forget; they know exactly what the Cybermen are, and they know that conversion into a Cyberman can cost people the very things that make them human. She and Barnaby are then captured by a Cyberman, but they claim to have wandered away from the rest of the refugees, and it herds them back to the camp. As it does so, Barnaby looks into its blank eyes and realises just how empty they are. The refugees believe that they’re being taken to a medical base for vaccination shots, but the people coming back out are dazed and emotionless, as if they’ve already undergone the first stage of Cyber-conversion. Barnaby still doesn’t want to trust Samantha, but surrounded by Cybermen, he doesn’t know what to do -- and as he struggles with his conscience, the Cybermen march him and Samantha into a lift with the other refugees and take them to the “treatment” cells. Barnaby has lost his chance to escape, and despite himself, he’s afraid. But as the first stage of Cyber-conversion begins, that emotion ceases to trouble him. There is nothing to fear...